Overview

This script is one in a series of case studies to compare between the parametric and nonparameteric cellcycleR methods. For nonparameteric case, we use the wavelet smoother as it is likely more efficient compared to B-splines and LOESS smoothers.

Simulation Example

We present a scenario where the genes behave sinusoidally. In this set up, the sinusoidal cellcyleR and the nonparameteric cellcycleR should behave more or less equivalently.

library(cellcycleR)
library(wavethresh)
## Loading required package: MASS
## WaveThresh: R wavelet software, release 4.6.6, installed
## 
## Copyright Guy Nason and others 1993-2013
## 
## Note: nlevels has been renamed to nlevelsWT
G <- 100;
num_cells <- 256;
amp_genes <- rep(10, G);
phi_genes <- rep(c(2,5), each=G/2);
sigma_genes <- rchisq(G, 4);
cell_times_sim <- seq(0,2*pi, length.out=num_cells);
cycle_data <- sim_sinusoidal_cycle(G, amp_genes, phi_genes, sigma_genes, cell_times_sim);

celltime_levels <- 256;

sample_reorder <- sample(1:num_cells,num_cells, replace=FALSE);
cell_times_reorder <- cell_times_sim[sample_reorder];
cycle_data_reorder <- cycle_data[sample_reorder,];

Sinusoidal cellcycleR

system.time(out_sinusoidal <- sin_cell_ordering_class(cycle_data_reorder, celltime_levels = 256, num_iter=500))
## The loglikelihood after iter 1 is: -89129.6788379 
## The loglikelihood after iter 2 is: -72366.5514278 
## The loglikelihood after iter 3 is: -67720.4637218 
## The loglikelihood after iter 4 is: -66528.2542913 
## The loglikelihood after iter 5 is: -65611.4992876 
## The loglikelihood after iter 6 is: -65218.1310939 
## The loglikelihood after iter 7 is: -65106.4963555 
## The loglikelihood after iter 8 is: -65037.8725019 
## The loglikelihood after iter 9 is: -64991.2023463 
## The loglikelihood after iter 10 is: -64947.4255798 
## The loglikelihood after iter 11 is: -64918.9365227 
## The loglikelihood after iter 12 is: -64905.9287575 
## The loglikelihood after iter 13 is: -64912.3772457 
## The loglikelihood after iter 14 is: -64914.4775689 
## The loglikelihood after iter 15 is: -64890.1103064 
## The loglikelihood after iter 16 is: -64879.5371202 
## The loglikelihood after iter 17 is: -64879.7176879 
## The loglikelihood after iter 18 is: -64912.7248652 
## The loglikelihood after iter 19 is: -64895.2969143 
## The loglikelihood after iter 20 is: -64887.727561 
## The loglikelihood after iter 21 is: -64891.269815 
## The loglikelihood after iter 22 is: -64874.8082944 
## The loglikelihood after iter 23 is: -64883.7809221 
## The loglikelihood after iter 24 is: -64863.6161374 
## The loglikelihood after iter 25 is: -64889.9289116 
## The loglikelihood after iter 26 is: -64870.6266703 
## The loglikelihood after iter 27 is: -64854.564381 
## The loglikelihood after iter 28 is: -64881.1861635 
## The loglikelihood after iter 29 is: -64871.025342 
## The loglikelihood after iter 30 is: -64874.8720158 
## The loglikelihood after iter 31 is: -64889.8722092 
## The loglikelihood after iter 32 is: -64868.5388292 
## The loglikelihood after iter 33 is: -64871.6518747 
## The loglikelihood after iter 34 is: -64863.1538594 
## The loglikelihood after iter 35 is: -64861.1111317 
## The loglikelihood after iter 36 is: -64856.482143 
## The loglikelihood after iter 37 is: -64891.6409745 
## The loglikelihood after iter 38 is: -64890.5310328 
## The loglikelihood after iter 39 is: -64865.3330975 
## The loglikelihood after iter 40 is: -64864.6461099 
## The loglikelihood after iter 41 is: -64847.9914439 
## The loglikelihood after iter 42 is: -64856.8780472 
## The loglikelihood after iter 43 is: -64851.2348701 
## The loglikelihood after iter 44 is: -64873.5631965 
## The loglikelihood after iter 45 is: -64863.7993801 
## The loglikelihood after iter 46 is: -64861.9002215 
## The loglikelihood after iter 47 is: -64853.1575015 
## The loglikelihood after iter 48 is: -64855.4009277 
## The loglikelihood after iter 49 is: -64834.9497842 
## The loglikelihood after iter 50 is: -64840.1611327 
## The loglikelihood after iter 51 is: -64858.0140423 
## The loglikelihood after iter 52 is: -64852.4953784 
## The loglikelihood after iter 53 is: -64862.5713434 
## The loglikelihood after iter 54 is: -64849.290437 
## The loglikelihood after iter 55 is: -64859.7413269 
## The loglikelihood after iter 56 is: -64842.5416935 
## The loglikelihood after iter 57 is: -64841.9220693 
## The loglikelihood after iter 58 is: -64851.8834124 
## The loglikelihood after iter 59 is: -64841.2278375 
## The loglikelihood after iter 60 is: -64854.1442124 
## The loglikelihood after iter 61 is: -64870.6025989 
## The loglikelihood after iter 62 is: -64862.4259181 
## The loglikelihood after iter 63 is: -64877.1334034 
## The loglikelihood after iter 64 is: -64865.5253617 
## The loglikelihood after iter 65 is: -64869.2186647 
## The loglikelihood after iter 66 is: -64875.0325014 
## The loglikelihood after iter 67 is: -64850.2387094 
## The loglikelihood after iter 68 is: -64856.0526282 
## The loglikelihood after iter 69 is: -64863.470679 
## The loglikelihood after iter 70 is: -64871.9213072 
## The loglikelihood after iter 71 is: -64892.9021885 
## The loglikelihood after iter 72 is: -64888.8134606 
## The loglikelihood after iter 73 is: -64874.3079282 
## The loglikelihood after iter 74 is: -64868.1240149 
## The loglikelihood after iter 75 is: -64873.8763203 
## The loglikelihood after iter 76 is: -64880.2471388 
## The loglikelihood after iter 77 is: -64861.2828649 
## The loglikelihood after iter 78 is: -64865.5212818 
## The loglikelihood after iter 79 is: -64870.4114492 
## The loglikelihood after iter 80 is: -64852.2756074 
## The loglikelihood after iter 81 is: -64860.0507067 
## The loglikelihood after iter 82 is: -64865.389491 
## The loglikelihood after iter 83 is: -64890.6476658 
## The loglikelihood after iter 84 is: -64858.638229 
## The loglikelihood after iter 85 is: -64886.4898371 
## The loglikelihood after iter 86 is: -64871.3480262 
## The loglikelihood after iter 87 is: -64869.6376491 
## The loglikelihood after iter 88 is: -64875.4222996 
## The loglikelihood after iter 89 is: -64861.4746327 
## The loglikelihood after iter 90 is: -64874.2205958 
## The loglikelihood after iter 91 is: -64879.7471666 
## The loglikelihood after iter 92 is: -64855.5500828 
## The loglikelihood after iter 93 is: -64862.7540504 
## The loglikelihood after iter 94 is: -64852.8003828 
## The loglikelihood after iter 95 is: -64881.4612938 
## The loglikelihood after iter 96 is: -64878.1498975 
## The loglikelihood after iter 97 is: -64885.1389285 
## The loglikelihood after iter 98 is: -64911.031703 
## The loglikelihood after iter 99 is: -64880.1381331 
## The loglikelihood after iter 100 is: -64886.9101708 
## The loglikelihood after iter 101 is: -64896.9393752 
## The loglikelihood after iter 102 is: -64877.6552763 
## The loglikelihood after iter 103 is: -64869.2496634 
## The loglikelihood after iter 104 is: -64868.9075614 
## The loglikelihood after iter 105 is: -64867.0779345 
## The loglikelihood after iter 106 is: -64858.473556 
## The loglikelihood after iter 107 is: -64869.0541068 
## The loglikelihood after iter 108 is: -64848.2144187 
## The loglikelihood after iter 109 is: -64881.5399286 
## The loglikelihood after iter 110 is: -64863.5707652 
## The loglikelihood after iter 111 is: -64852.4525506 
## The loglikelihood after iter 112 is: -64881.8651439 
## The loglikelihood after iter 113 is: -64861.4696308 
## The loglikelihood after iter 114 is: -64858.6463938 
## The loglikelihood after iter 115 is: -64858.2118468 
## The loglikelihood after iter 116 is: -64842.0188399 
## The loglikelihood after iter 117 is: -64840.4857757 
## The loglikelihood after iter 118 is: -64853.8250203 
## The loglikelihood after iter 119 is: -64858.0731982 
## The loglikelihood after iter 120 is: -64864.4097291 
## The loglikelihood after iter 121 is: -64872.6455523 
## The loglikelihood after iter 122 is: -64869.3976557 
## The loglikelihood after iter 123 is: -64857.5184188 
## The loglikelihood after iter 124 is: -64866.083446 
## The loglikelihood after iter 125 is: -64892.0514191 
## The loglikelihood after iter 126 is: -64855.8841351 
## The loglikelihood after iter 127 is: -64843.1296102 
## The loglikelihood after iter 128 is: -64859.3220718 
## The loglikelihood after iter 129 is: -64859.6821324 
## The loglikelihood after iter 130 is: -64865.1792207 
## The loglikelihood after iter 131 is: -64864.6356533 
## The loglikelihood after iter 132 is: -64859.7925332 
## The loglikelihood after iter 133 is: -64875.9162949 
## The loglikelihood after iter 134 is: -64855.0981087 
## The loglikelihood after iter 135 is: -64874.7113014 
## The loglikelihood after iter 136 is: -64879.9477506 
## The loglikelihood after iter 137 is: -64879.8312846 
## The loglikelihood after iter 138 is: -64862.5168328 
## The loglikelihood after iter 139 is: -64884.7770937 
## The loglikelihood after iter 140 is: -64864.055209 
## The loglikelihood after iter 141 is: -64864.9035521 
## The loglikelihood after iter 142 is: -64866.5737062 
## The loglikelihood after iter 143 is: -64873.3507195 
## The loglikelihood after iter 144 is: -64877.8191511 
## The loglikelihood after iter 145 is: -64867.5472108 
## The loglikelihood after iter 146 is: -64850.1481871 
## The loglikelihood after iter 147 is: -64870.5205501 
## The loglikelihood after iter 148 is: -64853.2570141 
## The loglikelihood after iter 149 is: -64855.1066326 
## The loglikelihood after iter 150 is: -64849.6883864 
## The loglikelihood after iter 151 is: -64862.3770601 
## The loglikelihood after iter 152 is: -64865.1380937 
## The loglikelihood after iter 153 is: -64867.7890685 
## The loglikelihood after iter 154 is: -64869.0194408 
## The loglikelihood after iter 155 is: -64861.2156923 
## The loglikelihood after iter 156 is: -64862.5470883 
## The loglikelihood after iter 157 is: -64862.7584068 
## The loglikelihood after iter 158 is: -64887.8719057 
## The loglikelihood after iter 159 is: -64871.1611443 
## The loglikelihood after iter 160 is: -64868.1747527 
## The loglikelihood after iter 161 is: -64882.5104528 
## The loglikelihood after iter 162 is: -64864.9521852 
## The loglikelihood after iter 163 is: -64848.4335113 
## The loglikelihood after iter 164 is: -64850.063511 
## The loglikelihood after iter 165 is: -64843.3810808 
## The loglikelihood after iter 166 is: -64857.7317401 
## The loglikelihood after iter 167 is: -64859.273769 
## The loglikelihood after iter 168 is: -64846.7002153 
## The loglikelihood after iter 169 is: -64838.9358339 
## The loglikelihood after iter 170 is: -64850.7654461 
## The loglikelihood after iter 171 is: -64849.9117013 
## The loglikelihood after iter 172 is: -64859.3574754 
## The loglikelihood after iter 173 is: -64852.1480753 
## The loglikelihood after iter 174 is: -64865.9741582 
## The loglikelihood after iter 175 is: -64880.2214967 
## The loglikelihood after iter 176 is: -64868.5575673 
## The loglikelihood after iter 177 is: -64865.6666025 
## The loglikelihood after iter 178 is: -64874.110936 
## The loglikelihood after iter 179 is: -64862.4203905 
## The loglikelihood after iter 180 is: -64850.0390285 
## The loglikelihood after iter 181 is: -64846.3680021 
## The loglikelihood after iter 182 is: -64856.0041151 
## The loglikelihood after iter 183 is: -64884.0020047 
## The loglikelihood after iter 184 is: -64881.7397862 
## The loglikelihood after iter 185 is: -64873.4631575 
## The loglikelihood after iter 186 is: -64852.5971107 
## The loglikelihood after iter 187 is: -64835.3274388 
## The loglikelihood after iter 188 is: -64840.390776 
## The loglikelihood after iter 189 is: -64841.3715702 
## The loglikelihood after iter 190 is: -64835.3453102 
## The loglikelihood after iter 191 is: -64832.1604688 
## The loglikelihood after iter 192 is: -64854.2534987 
## The loglikelihood after iter 193 is: -64848.009074 
## The loglikelihood after iter 194 is: -64849.578282 
## The loglikelihood after iter 195 is: -64844.1924528 
## The loglikelihood after iter 196 is: -64856.5947189 
## The loglikelihood after iter 197 is: -64856.566291 
## The loglikelihood after iter 198 is: -64847.307568 
## The loglikelihood after iter 199 is: -64853.5483173 
## The loglikelihood after iter 200 is: -64860.4231838 
## The loglikelihood after iter 201 is: -64875.5515372 
## The loglikelihood after iter 202 is: -64850.4593467 
## The loglikelihood after iter 203 is: -64849.2046574 
## The loglikelihood after iter 204 is: -64849.2897371 
## The loglikelihood after iter 205 is: -64865.0677322 
## The loglikelihood after iter 206 is: -64835.2450032 
## The loglikelihood after iter 207 is: -64852.1680772 
## The loglikelihood after iter 208 is: -64847.5614696 
## The loglikelihood after iter 209 is: -64830.852447 
## The loglikelihood after iter 210 is: -64820.618744 
## The loglikelihood after iter 211 is: -64855.5286049 
## The loglikelihood after iter 212 is: -64827.3804744 
## The loglikelihood after iter 213 is: -64854.1784523 
## The loglikelihood after iter 214 is: -64853.5046858 
## The loglikelihood after iter 215 is: -64859.9655603 
## The loglikelihood after iter 216 is: -64849.2851975 
## The loglikelihood after iter 217 is: -64865.276812 
## The loglikelihood after iter 218 is: -64847.4697974 
## The loglikelihood after iter 219 is: -64864.995278 
## The loglikelihood after iter 220 is: -64868.619922 
## The loglikelihood after iter 221 is: -64864.7225509 
## The loglikelihood after iter 222 is: -64869.2558831 
## The loglikelihood after iter 223 is: -64863.7343368 
## The loglikelihood after iter 224 is: -64858.3259208 
## The loglikelihood after iter 225 is: -64865.3410327 
## The loglikelihood after iter 226 is: -64882.79789 
## The loglikelihood after iter 227 is: -64894.0195316 
## The loglikelihood after iter 228 is: -64900.4693187 
## The loglikelihood after iter 229 is: -64881.5583861 
## The loglikelihood after iter 230 is: -64878.2258897 
## The loglikelihood after iter 231 is: -64850.5696499 
## The loglikelihood after iter 232 is: -64882.1788644 
## The loglikelihood after iter 233 is: -64892.4645229 
## The loglikelihood after iter 234 is: -64888.6145871 
## The loglikelihood after iter 235 is: -64872.1111395 
## The loglikelihood after iter 236 is: -64893.5558428 
## The loglikelihood after iter 237 is: -64870.4574227 
## The loglikelihood after iter 238 is: -64871.2437536 
## The loglikelihood after iter 239 is: -64885.1117573 
## The loglikelihood after iter 240 is: -64870.9211031 
## The loglikelihood after iter 241 is: -64860.214374 
## The loglikelihood after iter 242 is: -64868.3266672 
## The loglikelihood after iter 243 is: -64853.1835259 
## The loglikelihood after iter 244 is: -64865.2209189 
## The loglikelihood after iter 245 is: -64866.4694546 
## The loglikelihood after iter 246 is: -64858.0714884 
## The loglikelihood after iter 247 is: -64871.2704833 
## The loglikelihood after iter 248 is: -64868.536039 
## The loglikelihood after iter 249 is: -64876.3742201 
## The loglikelihood after iter 250 is: -64868.3044715 
## The loglikelihood after iter 251 is: -64857.522362 
## The loglikelihood after iter 252 is: -64865.6296763 
## The loglikelihood after iter 253 is: -64857.7688517 
## The loglikelihood after iter 254 is: -64883.3508497 
## The loglikelihood after iter 255 is: -64875.1880849 
## The loglikelihood after iter 256 is: -64858.7543776 
## The loglikelihood after iter 257 is: -64870.4972451 
## The loglikelihood after iter 258 is: -64870.4097822 
## The loglikelihood after iter 259 is: -64848.4970921 
## The loglikelihood after iter 260 is: -64848.4832829 
## The loglikelihood after iter 261 is: -64853.3237369 
## The loglikelihood after iter 262 is: -64842.3561316 
## The loglikelihood after iter 263 is: -64856.6551101 
## The loglikelihood after iter 264 is: -64871.304086 
## The loglikelihood after iter 265 is: -64854.8123195 
## The loglikelihood after iter 266 is: -64874.2020147 
## The loglikelihood after iter 267 is: -64870.4163019 
## The loglikelihood after iter 268 is: -64881.9702677 
## The loglikelihood after iter 269 is: -64882.4332918 
## The loglikelihood after iter 270 is: -64866.878773 
## The loglikelihood after iter 271 is: -64854.8349828 
## The loglikelihood after iter 272 is: -64869.5641741 
## The loglikelihood after iter 273 is: -64873.6378008 
## The loglikelihood after iter 274 is: -64869.0079786 
## The loglikelihood after iter 275 is: -64887.0481305 
## The loglikelihood after iter 276 is: -64877.2105862 
## The loglikelihood after iter 277 is: -64889.3122284 
## The loglikelihood after iter 278 is: -64877.9998298 
## The loglikelihood after iter 279 is: -64883.1455894 
## The loglikelihood after iter 280 is: -64882.9954172 
## The loglikelihood after iter 281 is: -64863.2931783 
## The loglikelihood after iter 282 is: -64869.407847 
## The loglikelihood after iter 283 is: -64887.547275 
## The loglikelihood after iter 284 is: -64855.4092786 
## The loglikelihood after iter 285 is: -64873.2881278 
## The loglikelihood after iter 286 is: -64852.1251438 
## The loglikelihood after iter 287 is: -64854.2931292 
## The loglikelihood after iter 288 is: -64847.3160964 
## The loglikelihood after iter 289 is: -64844.8982138 
## The loglikelihood after iter 290 is: -64840.5356779 
## The loglikelihood after iter 291 is: -64846.8917831 
## The loglikelihood after iter 292 is: -64838.0217196 
## The loglikelihood after iter 293 is: -64875.4081327 
## The loglikelihood after iter 294 is: -64854.97428 
## The loglikelihood after iter 295 is: -64859.8714677 
## The loglikelihood after iter 296 is: -64856.1552976 
## The loglikelihood after iter 297 is: -64859.9318486 
## The loglikelihood after iter 298 is: -64858.1552399 
## The loglikelihood after iter 299 is: -64855.913317 
## The loglikelihood after iter 300 is: -64868.0736958 
## The loglikelihood after iter 301 is: -64865.8950004 
## The loglikelihood after iter 302 is: -64861.8599502 
## The loglikelihood after iter 303 is: -64848.3063559 
## The loglikelihood after iter 304 is: -64853.5579667 
## The loglikelihood after iter 305 is: -64871.0555751 
## The loglikelihood after iter 306 is: -64860.8835935 
## The loglikelihood after iter 307 is: -64846.2149018 
## The loglikelihood after iter 308 is: -64844.2943056 
## The loglikelihood after iter 309 is: -64867.7751571 
## The loglikelihood after iter 310 is: -64882.8949571 
## The loglikelihood after iter 311 is: -64871.2215959 
## The loglikelihood after iter 312 is: -64856.5212715 
## The loglikelihood after iter 313 is: -64854.0706319 
## The loglikelihood after iter 314 is: -64852.6182139 
## The loglikelihood after iter 315 is: -64878.496598 
## The loglikelihood after iter 316 is: -64848.1345215 
## The loglikelihood after iter 317 is: -64866.4547258 
## The loglikelihood after iter 318 is: -64823.0832255 
## The loglikelihood after iter 319 is: -64824.8677504 
## The loglikelihood after iter 320 is: -64842.906664 
## The loglikelihood after iter 321 is: -64877.6426697 
## The loglikelihood after iter 322 is: -64849.2246057 
## The loglikelihood after iter 323 is: -64858.6381311 
## The loglikelihood after iter 324 is: -64852.7863451 
## The loglikelihood after iter 325 is: -64864.0658142 
## The loglikelihood after iter 326 is: -64848.4722342 
## The loglikelihood after iter 327 is: -64856.1492581 
## The loglikelihood after iter 328 is: -64864.928195 
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## The loglikelihood after iter 330 is: -64845.8372562 
## The loglikelihood after iter 331 is: -64848.7259035 
## The loglikelihood after iter 332 is: -64864.1597163 
## The loglikelihood after iter 333 is: -64861.7483598 
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## The loglikelihood after iter 337 is: -64869.275436 
## The loglikelihood after iter 338 is: -64881.5285728 
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## The loglikelihood after iter 341 is: -64860.3980098 
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## The loglikelihood after iter 351 is: -64873.7971728 
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## The loglikelihood after iter 356 is: -64882.5627523 
## The loglikelihood after iter 357 is: -64881.0490439 
## The loglikelihood after iter 358 is: -64887.4261915 
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## The loglikelihood after iter 360 is: -64884.9258882 
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## The loglikelihood after iter 375 is: -64869.0710308 
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## The loglikelihood after iter 380 is: -64842.3140475 
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## The loglikelihood after iter 382 is: -64855.1270618 
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## The loglikelihood after iter 389 is: -64871.8792435 
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## The loglikelihood after iter 400 is: -64850.6721291 
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## The loglikelihood after iter 408 is: -64883.8354037 
## The loglikelihood after iter 409 is: -64873.7680607 
## The loglikelihood after iter 410 is: -64861.9149247 
## The loglikelihood after iter 411 is: -64889.5805023 
## The loglikelihood after iter 412 is: -64858.319965 
## The loglikelihood after iter 413 is: -64868.7483445 
## The loglikelihood after iter 414 is: -64863.3757106 
## The loglikelihood after iter 415 is: -64865.8469496 
## The loglikelihood after iter 416 is: -64883.0998233 
## The loglikelihood after iter 417 is: -64851.6214669 
## The loglikelihood after iter 418 is: -64876.0692488 
## The loglikelihood after iter 419 is: -64891.8770585 
## The loglikelihood after iter 420 is: -64879.9504377 
## The loglikelihood after iter 421 is: -64876.17836 
## The loglikelihood after iter 422 is: -64871.2523425 
## The loglikelihood after iter 423 is: -64867.9924136 
## The loglikelihood after iter 424 is: -64868.7943182 
## The loglikelihood after iter 425 is: -64862.1227478 
## The loglikelihood after iter 426 is: -64865.4458191 
## The loglikelihood after iter 427 is: -64894.7282655 
## The loglikelihood after iter 428 is: -64878.2880471 
## The loglikelihood after iter 429 is: -64875.7494376 
## The loglikelihood after iter 430 is: -64859.4456138 
## The loglikelihood after iter 431 is: -64853.8248451 
## The loglikelihood after iter 432 is: -64867.1906939 
## The loglikelihood after iter 433 is: -64881.9384182 
## The loglikelihood after iter 434 is: -64877.6975973 
## The loglikelihood after iter 435 is: -64877.4490619 
## The loglikelihood after iter 436 is: -64858.9310346 
## The loglikelihood after iter 437 is: -64878.8191596 
## The loglikelihood after iter 438 is: -64873.418141 
## The loglikelihood after iter 439 is: -64866.6768409 
## The loglikelihood after iter 440 is: -64870.7187176 
## The loglikelihood after iter 441 is: -64872.1598163 
## The loglikelihood after iter 442 is: -64878.833921 
## The loglikelihood after iter 443 is: -64873.4120269 
## The loglikelihood after iter 444 is: -64863.7125105 
## The loglikelihood after iter 445 is: -64879.3832255 
## The loglikelihood after iter 446 is: -64861.1259759 
## The loglikelihood after iter 447 is: -64864.7429597 
## The loglikelihood after iter 448 is: -64855.8933649 
## The loglikelihood after iter 449 is: -64876.1762959 
## The loglikelihood after iter 450 is: -64868.7225439 
## The loglikelihood after iter 451 is: -64895.9202646 
## The loglikelihood after iter 452 is: -64876.7239931 
## The loglikelihood after iter 453 is: -64865.193373 
## The loglikelihood after iter 454 is: -64870.6054018 
## The loglikelihood after iter 455 is: -64878.4035235 
## The loglikelihood after iter 456 is: -64875.7237078 
## The loglikelihood after iter 457 is: -64880.560173 
## The loglikelihood after iter 458 is: -64896.0717781 
## The loglikelihood after iter 459 is: -64863.670493 
## The loglikelihood after iter 460 is: -64867.0598365 
## The loglikelihood after iter 461 is: -64878.9215914 
## The loglikelihood after iter 462 is: -64870.1050978 
## The loglikelihood after iter 463 is: -64894.5142283 
## The loglikelihood after iter 464 is: -64882.0884549 
## The loglikelihood after iter 465 is: -64892.6582451 
## The loglikelihood after iter 466 is: -64890.63369 
## The loglikelihood after iter 467 is: -64864.8440157 
## The loglikelihood after iter 468 is: -64849.7150527 
## The loglikelihood after iter 469 is: -64849.6006477 
## The loglikelihood after iter 470 is: -64866.8796426 
## The loglikelihood after iter 471 is: -64866.1823045 
## The loglikelihood after iter 472 is: -64886.668089 
## The loglikelihood after iter 473 is: -64882.0885998 
## The loglikelihood after iter 474 is: -64879.0549704 
## The loglikelihood after iter 475 is: -64885.8465152 
## The loglikelihood after iter 476 is: -64843.639402 
## The loglikelihood after iter 477 is: -64847.2097981 
## The loglikelihood after iter 478 is: -64873.8077299 
## The loglikelihood after iter 479 is: -64857.940929 
## The loglikelihood after iter 480 is: -64846.7754689 
## The loglikelihood after iter 481 is: -64859.2200455 
## The loglikelihood after iter 482 is: -64873.3344607 
## The loglikelihood after iter 483 is: -64862.6105314 
## The loglikelihood after iter 484 is: -64868.6120828 
## The loglikelihood after iter 485 is: -64875.1319361 
## The loglikelihood after iter 486 is: -64867.1219738 
## The loglikelihood after iter 487 is: -64874.2295332 
## The loglikelihood after iter 488 is: -64866.7257299 
## The loglikelihood after iter 489 is: -64856.3512946 
## The loglikelihood after iter 490 is: -64861.8085573 
## The loglikelihood after iter 491 is: -64845.8246435 
## The loglikelihood after iter 492 is: -64856.3013461 
## The loglikelihood after iter 493 is: -64852.3467296 
## The loglikelihood after iter 494 is: -64872.1593494 
## The loglikelihood after iter 495 is: -64865.8626453 
## The loglikelihood after iter 496 is: -64877.0886089 
## The loglikelihood after iter 497 is: -64875.0014068 
## The loglikelihood after iter 498 is: -64875.0535544 
## The loglikelihood after iter 499 is: -64891.1798426 
## The loglikelihood after iter 500 is: -64884.1474973
##    user  system elapsed 
## 805.100 271.688 417.628
library(plotrix)
## Warning: package 'plotrix' was built under R version 3.2.3
library(RColorBrewer)
radial.plot(lengths=1:length(out_sinusoidal$cell_times),radial.pos=out_sinusoidal$cell_times[order(cell_times_reorder)],
            line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(out_sinusoidal$cell_times)), lwd=2)

radial.plot(lengths=1:length(cell_times_reorder),radial.pos=sort(cell_times_reorder),
            line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(cell_times_reorder)), lwd=2)

The plots of estimated gene pattern and the true gene pattern.

First co-ordinate

plot(cycle_data_reorder[order(out_sinusoidal$cell_times),1], type="l")

plot(cycle_data[,1],type="l")

30th coordinate

plot(cycle_data_reorder[order(out_sinusoidal$cell_times),30], type="l")

plot(cycle_data[,30],type="l")

50th coordinate

plot(cycle_data_reorder[order(out_sinusoidal$cell_times),50], type="l")

plot(cycle_data[,50],type="l")

Nonparametric cellcycleR

system.time(out_np <- np_cell_ordering_class(cycle_data_reorder, celltime_levels = 256, num_iter=500))
## The loglikelihood after iter 1 is: -87298.0168882 
## The loglikelihood after iter 2 is: -82210.903661 
## The loglikelihood after iter 3 is: -81732.0910989 
## The loglikelihood after iter 4 is: -81487.8849242 
## The loglikelihood after iter 5 is: -81465.2739655 
## The loglikelihood after iter 6 is: -81488.862497 
## The loglikelihood after iter 7 is: -81420.0458951 
## The loglikelihood after iter 8 is: -81381.197913 
## The loglikelihood after iter 9 is: -81334.3208291 
## The loglikelihood after iter 10 is: -81285.5230018 
## The loglikelihood after iter 11 is: -81274.3254315 
## The loglikelihood after iter 12 is: -81264.4587811 
## The loglikelihood after iter 13 is: -81241.8815628 
## The loglikelihood after iter 14 is: -81267.6164699 
## The loglikelihood after iter 15 is: -81291.1605353 
## The loglikelihood after iter 16 is: -81287.7479082 
## The loglikelihood after iter 17 is: -81291.5661111 
## The loglikelihood after iter 18 is: -81284.6798207 
## The loglikelihood after iter 19 is: -81276.5218061 
## The loglikelihood after iter 20 is: -81266.2361375 
## The loglikelihood after iter 21 is: -81275.2721449 
## The loglikelihood after iter 22 is: -81273.1477923 
## The loglikelihood after iter 23 is: -81258.5728768 
## The loglikelihood after iter 24 is: -81278.2672374 
## The loglikelihood after iter 25 is: -81258.4130539 
## The loglikelihood after iter 26 is: -81288.132209 
## The loglikelihood after iter 27 is: -81253.1405194 
## The loglikelihood after iter 28 is: -81256.6824343 
## The loglikelihood after iter 29 is: -81266.6671089 
## The loglikelihood after iter 30 is: -81300.9709676 
## The loglikelihood after iter 31 is: -81280.2376023 
## The loglikelihood after iter 32 is: -81310.0716773 
## The loglikelihood after iter 33 is: -81265.9030412 
## The loglikelihood after iter 34 is: -81260.2758044 
## The loglikelihood after iter 35 is: -81271.7661272 
## The loglikelihood after iter 36 is: -81252.3675677 
## The loglikelihood after iter 37 is: -81273.864945 
## The loglikelihood after iter 38 is: -81273.3489174 
## The loglikelihood after iter 39 is: -81246.2591283 
## The loglikelihood after iter 40 is: -81246.5220314 
## The loglikelihood after iter 41 is: -81256.4117745 
## The loglikelihood after iter 42 is: -81278.1051255 
## The loglikelihood after iter 43 is: -81237.4959655 
## The loglikelihood after iter 44 is: -81263.4987052 
## The loglikelihood after iter 45 is: -81289.9008932 
## The loglikelihood after iter 46 is: -81286.4751028 
## The loglikelihood after iter 47 is: -81247.4802349 
## The loglikelihood after iter 48 is: -81263.950398 
## The loglikelihood after iter 49 is: -81258.0211919 
## The loglikelihood after iter 50 is: -81280.7913086 
## The loglikelihood after iter 51 is: -81264.5441904 
## The loglikelihood after iter 52 is: -81243.7811172 
## The loglikelihood after iter 53 is: -81273.7089367 
## The loglikelihood after iter 54 is: -81267.8388209 
## The loglikelihood after iter 55 is: -81265.6740946 
## The loglikelihood after iter 56 is: -81258.7782864 
## The loglikelihood after iter 57 is: -81253.9725622 
## The loglikelihood after iter 58 is: -81261.4133871 
## The loglikelihood after iter 59 is: -81276.1795048 
## The loglikelihood after iter 60 is: -81260.9387165 
## The loglikelihood after iter 61 is: -81283.7899742 
## The loglikelihood after iter 62 is: -81256.0244255 
## The loglikelihood after iter 63 is: -81252.7779563 
## The loglikelihood after iter 64 is: -81250.6674598 
## The loglikelihood after iter 65 is: -81233.2127246 
## The loglikelihood after iter 66 is: -81260.3174931 
## The loglikelihood after iter 67 is: -81271.7572472 
## The loglikelihood after iter 68 is: -81281.8930446 
## The loglikelihood after iter 69 is: -81261.2006999 
## The loglikelihood after iter 70 is: -81277.3376784 
## The loglikelihood after iter 71 is: -81245.4406282 
## The loglikelihood after iter 72 is: -81268.3055364 
## The loglikelihood after iter 73 is: -81259.9160351 
## The loglikelihood after iter 74 is: -81260.9018865 
## The loglikelihood after iter 75 is: -81238.492466 
## The loglikelihood after iter 76 is: -81269.3884208 
## The loglikelihood after iter 77 is: -81250.1265451 
## The loglikelihood after iter 78 is: -81242.0457633 
## The loglikelihood after iter 79 is: -81263.3053532 
## The loglikelihood after iter 80 is: -81236.7750625 
## The loglikelihood after iter 81 is: -81255.7412326 
## The loglikelihood after iter 82 is: -81273.9516319 
## The loglikelihood after iter 83 is: -81265.5865135 
## The loglikelihood after iter 84 is: -81271.1405008 
## The loglikelihood after iter 85 is: -81266.5155584 
## The loglikelihood after iter 86 is: -81274.8601959 
## The loglikelihood after iter 87 is: -81258.2034256 
## The loglikelihood after iter 88 is: -81258.6452145 
## The loglikelihood after iter 89 is: -81284.4270604 
## The loglikelihood after iter 90 is: -81251.6978414 
## The loglikelihood after iter 91 is: -81272.5026904 
## The loglikelihood after iter 92 is: -81279.7035021 
## The loglikelihood after iter 93 is: -81291.4940687 
## The loglikelihood after iter 94 is: -81253.1211012 
## The loglikelihood after iter 95 is: -81236.2477305 
## The loglikelihood after iter 96 is: -81266.2105582 
## The loglikelihood after iter 97 is: -81262.1571036 
## The loglikelihood after iter 98 is: -81284.4513284 
## The loglikelihood after iter 99 is: -81255.240332 
## The loglikelihood after iter 100 is: -81234.9903731 
## The loglikelihood after iter 101 is: -81244.2527008 
## The loglikelihood after iter 102 is: -81253.7031625 
## The loglikelihood after iter 103 is: -81251.4460411 
## The loglikelihood after iter 104 is: -81264.2829316 
## The loglikelihood after iter 105 is: -81256.4176671 
## The loglikelihood after iter 106 is: -81233.5361085 
## The loglikelihood after iter 107 is: -81261.6250862 
## The loglikelihood after iter 108 is: -81273.9403068 
## The loglikelihood after iter 109 is: -81266.1143819 
## The loglikelihood after iter 110 is: -81270.7898476 
## The loglikelihood after iter 111 is: -81265.3717196 
## The loglikelihood after iter 112 is: -81272.9264378 
## The loglikelihood after iter 113 is: -81303.6715576 
## The loglikelihood after iter 114 is: -81278.1211624 
## The loglikelihood after iter 115 is: -81269.1128057 
## The loglikelihood after iter 116 is: -81263.0638972 
## The loglikelihood after iter 117 is: -81267.4177177 
## The loglikelihood after iter 118 is: -81273.2852476 
## The loglikelihood after iter 119 is: -81239.2728788 
## The loglikelihood after iter 120 is: -81285.2523283 
## The loglikelihood after iter 121 is: -81264.0957287 
## The loglikelihood after iter 122 is: -81250.9047587 
## The loglikelihood after iter 123 is: -81253.1587199 
## The loglikelihood after iter 124 is: -81258.8427118 
## The loglikelihood after iter 125 is: -81256.0022117 
## The loglikelihood after iter 126 is: -81264.4473962 
## The loglikelihood after iter 127 is: -81272.784537 
## The loglikelihood after iter 128 is: -81276.7613465 
## The loglikelihood after iter 129 is: -81278.976355 
## The loglikelihood after iter 130 is: -81291.3295354 
## The loglikelihood after iter 131 is: -81254.7741262 
## The loglikelihood after iter 132 is: -81246.6105079 
## The loglikelihood after iter 133 is: -81255.1420651 
## The loglikelihood after iter 134 is: -81261.0556348 
## The loglikelihood after iter 135 is: -81255.9765365 
## The loglikelihood after iter 136 is: -81263.8169238 
## The loglikelihood after iter 137 is: -81284.0290383 
## The loglikelihood after iter 138 is: -81261.5187647 
## The loglikelihood after iter 139 is: -81291.8308653 
## The loglikelihood after iter 140 is: -81256.9220922 
## The loglikelihood after iter 141 is: -81267.7866796 
## The loglikelihood after iter 142 is: -81249.5651857 
## The loglikelihood after iter 143 is: -81273.5777835 
## The loglikelihood after iter 144 is: -81267.0585758 
## The loglikelihood after iter 145 is: -81294.8784343 
## The loglikelihood after iter 146 is: -81289.8171784 
## The loglikelihood after iter 147 is: -81292.416951 
## The loglikelihood after iter 148 is: -81281.8192351 
## The loglikelihood after iter 149 is: -81273.4365277 
## The loglikelihood after iter 150 is: -81267.3247234 
## The loglikelihood after iter 151 is: -81259.3860988 
## The loglikelihood after iter 152 is: -81252.8673205 
## The loglikelihood after iter 153 is: -81268.5309725 
## The loglikelihood after iter 154 is: -81260.7560101 
## The loglikelihood after iter 155 is: -81256.3599612 
## The loglikelihood after iter 156 is: -81271.0201481 
## The loglikelihood after iter 157 is: -81303.6452485 
## The loglikelihood after iter 158 is: -81272.7819976 
## The loglikelihood after iter 159 is: -81257.2150193 
## The loglikelihood after iter 160 is: -81278.0627131 
## The loglikelihood after iter 161 is: -81250.2848226 
## The loglikelihood after iter 162 is: -81253.3273024 
## The loglikelihood after iter 163 is: -81244.9682435 
## The loglikelihood after iter 164 is: -81253.5081788 
## The loglikelihood after iter 165 is: -81259.8245875 
## The loglikelihood after iter 166 is: -81256.6791554 
## The loglikelihood after iter 167 is: -81260.1986247 
## The loglikelihood after iter 168 is: -81269.9855413 
## The loglikelihood after iter 169 is: -81271.6706054 
## The loglikelihood after iter 170 is: -81260.9473048 
## The loglikelihood after iter 171 is: -81264.809026 
## The loglikelihood after iter 172 is: -81243.0971849 
## The loglikelihood after iter 173 is: -81282.1568065 
## The loglikelihood after iter 174 is: -81246.2993207 
## The loglikelihood after iter 175 is: -81230.134453 
## The loglikelihood after iter 176 is: -81249.3199527 
## The loglikelihood after iter 177 is: -81259.2353235 
## The loglikelihood after iter 178 is: -81267.4745049 
## The loglikelihood after iter 179 is: -81244.3630801 
## The loglikelihood after iter 180 is: -81291.3028774 
## The loglikelihood after iter 181 is: -81252.522268 
## The loglikelihood after iter 182 is: -81268.6371363 
## The loglikelihood after iter 183 is: -81267.1377231 
## The loglikelihood after iter 184 is: -81262.9683088 
## The loglikelihood after iter 185 is: -81257.2994219 
## The loglikelihood after iter 186 is: -81257.2832241 
## The loglikelihood after iter 187 is: -81235.0898399 
## The loglikelihood after iter 188 is: -81274.018001 
## The loglikelihood after iter 189 is: -81270.3845343 
## The loglikelihood after iter 190 is: -81259.8987896 
## The loglikelihood after iter 191 is: -81287.2663184 
## The loglikelihood after iter 192 is: -81273.7708858 
## The loglikelihood after iter 193 is: -81282.126664 
## The loglikelihood after iter 194 is: -81270.4632616 
## The loglikelihood after iter 195 is: -81268.7183867 
## The loglikelihood after iter 196 is: -81266.6823362 
## The loglikelihood after iter 197 is: -81290.9317733 
## The loglikelihood after iter 198 is: -81303.7145713 
## The loglikelihood after iter 199 is: -81275.026992 
## The loglikelihood after iter 200 is: -81266.3966687 
## The loglikelihood after iter 201 is: -81248.5888244 
## The loglikelihood after iter 202 is: -81272.7769343 
## The loglikelihood after iter 203 is: -81254.5856908 
## The loglikelihood after iter 204 is: -81274.4171964 
## The loglikelihood after iter 205 is: -81257.669748 
## The loglikelihood after iter 206 is: -81257.0560567 
## The loglikelihood after iter 207 is: -81253.9680549 
## The loglikelihood after iter 208 is: -81238.3233434 
## The loglikelihood after iter 209 is: -81259.0669025 
## The loglikelihood after iter 210 is: -81272.1745434 
## The loglikelihood after iter 211 is: -81273.5437873 
## The loglikelihood after iter 212 is: -81234.6534862 
## The loglikelihood after iter 213 is: -81253.7565296 
## The loglikelihood after iter 214 is: -81245.4945506 
## The loglikelihood after iter 215 is: -81246.7249528 
## The loglikelihood after iter 216 is: -81254.2480945 
## The loglikelihood after iter 217 is: -81258.3701743 
## The loglikelihood after iter 218 is: -81263.6641702 
## The loglikelihood after iter 219 is: -81258.0058696 
## The loglikelihood after iter 220 is: -81285.2997019 
## The loglikelihood after iter 221 is: -81261.1510016 
## The loglikelihood after iter 222 is: -81262.2643081 
## The loglikelihood after iter 223 is: -81283.554423 
## The loglikelihood after iter 224 is: -81264.8013992 
## The loglikelihood after iter 225 is: -81264.830812 
## The loglikelihood after iter 226 is: -81288.2371956 
## The loglikelihood after iter 227 is: -81283.2635219 
## The loglikelihood after iter 228 is: -81264.1097759 
## The loglikelihood after iter 229 is: -81274.3545137 
## The loglikelihood after iter 230 is: -81239.6742113 
## The loglikelihood after iter 231 is: -81256.1822176 
## The loglikelihood after iter 232 is: -81264.3117324 
## The loglikelihood after iter 233 is: -81252.528402 
## The loglikelihood after iter 234 is: -81284.2562481 
## The loglikelihood after iter 235 is: -81242.1327198 
## The loglikelihood after iter 236 is: -81268.5710285 
## The loglikelihood after iter 237 is: -81257.607077 
## The loglikelihood after iter 238 is: -81270.7375313 
## The loglikelihood after iter 239 is: -81277.5463552 
## The loglikelihood after iter 240 is: -81264.9686574 
## The loglikelihood after iter 241 is: -81294.0353916 
## The loglikelihood after iter 242 is: -81248.6414743 
## The loglikelihood after iter 243 is: -81263.2956175 
## The loglikelihood after iter 244 is: -81252.6192204 
## The loglikelihood after iter 245 is: -81265.4200847 
## The loglikelihood after iter 246 is: -81245.6915341 
## The loglikelihood after iter 247 is: -81236.6269826 
## The loglikelihood after iter 248 is: -81259.1344345 
## The loglikelihood after iter 249 is: -81257.7224607 
## The loglikelihood after iter 250 is: -81255.1579511 
## The loglikelihood after iter 251 is: -81251.4406083 
## The loglikelihood after iter 252 is: -81251.7364211 
## The loglikelihood after iter 253 is: -81256.5665786 
## The loglikelihood after iter 254 is: -81259.3616468 
## The loglikelihood after iter 255 is: -81248.071536 
## The loglikelihood after iter 256 is: -81254.3689798 
## The loglikelihood after iter 257 is: -81273.3966778 
## The loglikelihood after iter 258 is: -81270.2141616 
## The loglikelihood after iter 259 is: -81246.5740176 
## The loglikelihood after iter 260 is: -81263.1774216 
## The loglikelihood after iter 261 is: -81264.4592459 
## The loglikelihood after iter 262 is: -81252.9278678 
## The loglikelihood after iter 263 is: -81255.3674383 
## The loglikelihood after iter 264 is: -81252.0348196 
## The loglikelihood after iter 265 is: -81280.3210422 
## The loglikelihood after iter 266 is: -81275.3563019 
## The loglikelihood after iter 267 is: -81252.0344419 
## The loglikelihood after iter 268 is: -81280.0255033 
## The loglikelihood after iter 269 is: -81247.2922892 
## The loglikelihood after iter 270 is: -81282.3899709 
## The loglikelihood after iter 271 is: -81272.5848304 
## The loglikelihood after iter 272 is: -81255.8326559 
## The loglikelihood after iter 273 is: -81267.7778288 
## The loglikelihood after iter 274 is: -81255.7134831 
## The loglikelihood after iter 275 is: -81272.6010285 
## The loglikelihood after iter 276 is: -81245.9580961 
## The loglikelihood after iter 277 is: -81247.0528254 
## The loglikelihood after iter 278 is: -81232.0021505 
## The loglikelihood after iter 279 is: -81274.9845132 
## The loglikelihood after iter 280 is: -81278.5408426 
## The loglikelihood after iter 281 is: -81269.9634338 
## The loglikelihood after iter 282 is: -81267.2081042 
## The loglikelihood after iter 283 is: -81279.2154662 
## The loglikelihood after iter 284 is: -81273.4374362 
## The loglikelihood after iter 285 is: -81268.8447397 
## The loglikelihood after iter 286 is: -81253.0710106 
## The loglikelihood after iter 287 is: -81252.0926461 
## The loglikelihood after iter 288 is: -81275.858995 
## The loglikelihood after iter 289 is: -81250.0366915 
## The loglikelihood after iter 290 is: -81277.6986663 
## The loglikelihood after iter 291 is: -81267.0163809 
## The loglikelihood after iter 292 is: -81299.7091526 
## The loglikelihood after iter 293 is: -81282.4572055 
## The loglikelihood after iter 294 is: -81278.3218038 
## The loglikelihood after iter 295 is: -81298.6269399 
## The loglikelihood after iter 296 is: -81275.8791507 
## The loglikelihood after iter 297 is: -81295.155926 
## The loglikelihood after iter 298 is: -81268.9805193 
## The loglikelihood after iter 299 is: -81291.0357223 
## The loglikelihood after iter 300 is: -81275.583474 
## The loglikelihood after iter 301 is: -81261.3968239 
## The loglikelihood after iter 302 is: -81277.0073172 
## The loglikelihood after iter 303 is: -81251.3416696 
## The loglikelihood after iter 304 is: -81273.8617103 
## The loglikelihood after iter 305 is: -81286.6128985 
## The loglikelihood after iter 306 is: -81310.5081526 
## The loglikelihood after iter 307 is: -81276.7773581 
## The loglikelihood after iter 308 is: -81269.5820649 
## The loglikelihood after iter 309 is: -81268.8252465 
## The loglikelihood after iter 310 is: -81250.5468231 
## The loglikelihood after iter 311 is: -81226.4358028 
## The loglikelihood after iter 312 is: -81260.3487675 
## The loglikelihood after iter 313 is: -81271.2274893 
## The loglikelihood after iter 314 is: -81304.2752908 
## The loglikelihood after iter 315 is: -81263.6599241 
## The loglikelihood after iter 316 is: -81265.5864404 
## The loglikelihood after iter 317 is: -81264.8880915 
## The loglikelihood after iter 318 is: -81276.3806541 
## The loglikelihood after iter 319 is: -81297.9233204 
## The loglikelihood after iter 320 is: -81265.9324051 
## The loglikelihood after iter 321 is: -81288.5075036 
## The loglikelihood after iter 322 is: -81281.822364 
## The loglikelihood after iter 323 is: -81275.9506765 
## The loglikelihood after iter 324 is: -81268.3226518 
## The loglikelihood after iter 325 is: -81259.2963719 
## The loglikelihood after iter 326 is: -81261.9618339 
## The loglikelihood after iter 327 is: -81274.135844 
## The loglikelihood after iter 328 is: -81247.6691757 
## The loglikelihood after iter 329 is: -81251.5828148 
## The loglikelihood after iter 330 is: -81260.6973708 
## The loglikelihood after iter 331 is: -81260.1121368 
## The loglikelihood after iter 332 is: -81282.8496023 
## The loglikelihood after iter 333 is: -81277.4261092 
## The loglikelihood after iter 334 is: -81279.9357383 
## The loglikelihood after iter 335 is: -81262.7346823 
## The loglikelihood after iter 336 is: -81282.2541741 
## The loglikelihood after iter 337 is: -81268.6229245 
## The loglikelihood after iter 338 is: -81277.5012477 
## The loglikelihood after iter 339 is: -81287.7406626 
## The loglikelihood after iter 340 is: -81271.6492231 
## The loglikelihood after iter 341 is: -81282.4779611 
## The loglikelihood after iter 342 is: -81266.3046603 
## The loglikelihood after iter 343 is: -81281.8801214 
## The loglikelihood after iter 344 is: -81287.9131921 
## The loglikelihood after iter 345 is: -81266.1834085 
## The loglikelihood after iter 346 is: -81272.0960997 
## The loglikelihood after iter 347 is: -81285.7564543 
## The loglikelihood after iter 348 is: -81253.2459002 
## The loglikelihood after iter 349 is: -81274.9204674 
## The loglikelihood after iter 350 is: -81284.5212156 
## The loglikelihood after iter 351 is: -81272.8724603 
## The loglikelihood after iter 352 is: -81264.0151677 
## The loglikelihood after iter 353 is: -81261.202901 
## The loglikelihood after iter 354 is: -81273.6885002 
## The loglikelihood after iter 355 is: -81260.3716946 
## The loglikelihood after iter 356 is: -81261.5571763 
## The loglikelihood after iter 357 is: -81269.2590969 
## The loglikelihood after iter 358 is: -81269.9213342 
## The loglikelihood after iter 359 is: -81241.2695444 
## The loglikelihood after iter 360 is: -81258.2965749 
## The loglikelihood after iter 361 is: -81262.1729995 
## The loglikelihood after iter 362 is: -81274.5213325 
## The loglikelihood after iter 363 is: -81284.23637 
## The loglikelihood after iter 364 is: -81288.3918894 
## The loglikelihood after iter 365 is: -81289.5372333 
## The loglikelihood after iter 366 is: -81247.199798 
## The loglikelihood after iter 367 is: -81246.656289 
## The loglikelihood after iter 368 is: -81291.1866767 
## The loglikelihood after iter 369 is: -81310.5416623 
## The loglikelihood after iter 370 is: -81278.1134429 
## The loglikelihood after iter 371 is: -81264.0570621 
## The loglikelihood after iter 372 is: -81299.5912711 
## The loglikelihood after iter 373 is: -81284.9218594 
## The loglikelihood after iter 374 is: -81274.0360066 
## The loglikelihood after iter 375 is: -81259.7592992 
## The loglikelihood after iter 376 is: -81276.6947251 
## The loglikelihood after iter 377 is: -81288.4723421 
## The loglikelihood after iter 378 is: -81256.88244 
## The loglikelihood after iter 379 is: -81281.6413923 
## The loglikelihood after iter 380 is: -81298.0423314 
## The loglikelihood after iter 381 is: -81262.1993408 
## The loglikelihood after iter 382 is: -81258.846041 
## The loglikelihood after iter 383 is: -81273.431525 
## The loglikelihood after iter 384 is: -81287.7912621 
## The loglikelihood after iter 385 is: -81287.7019713 
## The loglikelihood after iter 386 is: -81268.1885533 
## The loglikelihood after iter 387 is: -81287.4464785 
## The loglikelihood after iter 388 is: -81289.7649246 
## The loglikelihood after iter 389 is: -81268.669882 
## The loglikelihood after iter 390 is: -81289.0961143 
## The loglikelihood after iter 391 is: -81290.043863 
## The loglikelihood after iter 392 is: -81285.241763 
## The loglikelihood after iter 393 is: -81265.682629 
## The loglikelihood after iter 394 is: -81277.5710085 
## The loglikelihood after iter 395 is: -81268.6620411 
## The loglikelihood after iter 396 is: -81272.8326414 
## The loglikelihood after iter 397 is: -81268.2921885 
## The loglikelihood after iter 398 is: -81266.7924475 
## The loglikelihood after iter 399 is: -81272.5111934 
## The loglikelihood after iter 400 is: -81257.577229 
## The loglikelihood after iter 401 is: -81248.4160191 
## The loglikelihood after iter 402 is: -81268.0374672 
## The loglikelihood after iter 403 is: -81268.8635811 
## The loglikelihood after iter 404 is: -81273.281243 
## The loglikelihood after iter 405 is: -81268.1761757 
## The loglikelihood after iter 406 is: -81263.6813687 
## The loglikelihood after iter 407 is: -81277.3055695 
## The loglikelihood after iter 408 is: -81242.2996807 
## The loglikelihood after iter 409 is: -81254.7269967 
## The loglikelihood after iter 410 is: -81258.3291591 
## The loglikelihood after iter 411 is: -81253.7011736 
## The loglikelihood after iter 412 is: -81257.5369003 
## The loglikelihood after iter 413 is: -81270.9482684 
## The loglikelihood after iter 414 is: -81251.7030927 
## The loglikelihood after iter 415 is: -81271.7664764 
## The loglikelihood after iter 416 is: -81257.5429595 
## The loglikelihood after iter 417 is: -81278.7467834 
## The loglikelihood after iter 418 is: -81278.7099194 
## The loglikelihood after iter 419 is: -81256.345915 
## The loglikelihood after iter 420 is: -81242.209909 
## The loglikelihood after iter 421 is: -81256.1756188 
## The loglikelihood after iter 422 is: -81273.8211432 
## The loglikelihood after iter 423 is: -81280.5023139 
## The loglikelihood after iter 424 is: -81273.1942058 
## The loglikelihood after iter 425 is: -81276.6483336 
## The loglikelihood after iter 426 is: -81270.7625584 
## The loglikelihood after iter 427 is: -81273.7631247 
## The loglikelihood after iter 428 is: -81263.2665321 
## The loglikelihood after iter 429 is: -81241.8903778 
## The loglikelihood after iter 430 is: -81276.4381014 
## The loglikelihood after iter 431 is: -81281.4520526 
## The loglikelihood after iter 432 is: -81249.2838388 
## The loglikelihood after iter 433 is: -81262.0669697 
## The loglikelihood after iter 434 is: -81257.2658372 
## The loglikelihood after iter 435 is: -81260.0059969 
## The loglikelihood after iter 436 is: -81259.4957203 
## The loglikelihood after iter 437 is: -81238.0024337 
## The loglikelihood after iter 438 is: -81244.3449868 
## The loglikelihood after iter 439 is: -81297.2536247 
## The loglikelihood after iter 440 is: -81266.9300965 
## The loglikelihood after iter 441 is: -81261.8734422 
## The loglikelihood after iter 442 is: -81267.428392 
## The loglikelihood after iter 443 is: -81273.3057824 
## The loglikelihood after iter 444 is: -81271.7363778 
## The loglikelihood after iter 445 is: -81271.6442337 
## The loglikelihood after iter 446 is: -81255.3793899 
## The loglikelihood after iter 447 is: -81276.276294 
## The loglikelihood after iter 448 is: -81267.2725703 
## The loglikelihood after iter 449 is: -81248.465112 
## The loglikelihood after iter 450 is: -81240.9439743 
## The loglikelihood after iter 451 is: -81289.1179393 
## The loglikelihood after iter 452 is: -81237.7945649 
## The loglikelihood after iter 453 is: -81262.4476301 
## The loglikelihood after iter 454 is: -81276.4495883 
## The loglikelihood after iter 455 is: -81262.8509395 
## The loglikelihood after iter 456 is: -81283.1077943 
## The loglikelihood after iter 457 is: -81282.3490456 
## The loglikelihood after iter 458 is: -81252.3128433 
## The loglikelihood after iter 459 is: -81264.9230006 
## The loglikelihood after iter 460 is: -81277.8244048 
## The loglikelihood after iter 461 is: -81264.4189101 
## The loglikelihood after iter 462 is: -81252.9407919 
## The loglikelihood after iter 463 is: -81275.3246797 
## The loglikelihood after iter 464 is: -81283.4263996 
## The loglikelihood after iter 465 is: -81259.8383306 
## The loglikelihood after iter 466 is: -81262.9920835 
## The loglikelihood after iter 467 is: -81259.6885449 
## The loglikelihood after iter 468 is: -81261.5845598 
## The loglikelihood after iter 469 is: -81231.1438407 
## The loglikelihood after iter 470 is: -81269.2179902 
## The loglikelihood after iter 471 is: -81297.6630656 
## The loglikelihood after iter 472 is: -81270.1469171 
## The loglikelihood after iter 473 is: -81265.5937865 
## The loglikelihood after iter 474 is: -81273.3540634 
## The loglikelihood after iter 475 is: -81276.8255592 
## The loglikelihood after iter 476 is: -81270.7647994 
## The loglikelihood after iter 477 is: -81271.3177334 
## The loglikelihood after iter 478 is: -81271.9150197 
## The loglikelihood after iter 479 is: -81283.7941287 
## The loglikelihood after iter 480 is: -81259.0819858 
## The loglikelihood after iter 481 is: -81296.5725339 
## The loglikelihood after iter 482 is: -81291.1945719 
## The loglikelihood after iter 483 is: -81285.7758821 
## The loglikelihood after iter 484 is: -81272.9944841 
## The loglikelihood after iter 485 is: -81254.6589313 
## The loglikelihood after iter 486 is: -81288.6605891 
## The loglikelihood after iter 487 is: -81279.0369632 
## The loglikelihood after iter 488 is: -81305.5948043 
## The loglikelihood after iter 489 is: -81281.3161315 
## The loglikelihood after iter 490 is: -81269.8547653 
## The loglikelihood after iter 491 is: -81266.3055526 
## The loglikelihood after iter 492 is: -81267.2313 
## The loglikelihood after iter 493 is: -81260.3359002 
## The loglikelihood after iter 494 is: -81263.7573833 
## The loglikelihood after iter 495 is: -81269.4914367 
## The loglikelihood after iter 496 is: -81262.2301243 
## The loglikelihood after iter 497 is: -81259.6054466 
## The loglikelihood after iter 498 is: -81283.1888847 
## The loglikelihood after iter 499 is: -81257.7028098 
## The loglikelihood after iter 500 is: -81281.7125924
##     user   system  elapsed 
## 1369.086  388.706  714.119
library(plotrix)
library(RColorBrewer)
radial.plot(lengths=1:length(out_np$cell_times),radial.pos=out_np$cell_times[order(cell_times_reorder)],
            line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(out_np$cell_times)), lwd=2)

radial.plot(lengths=1:length(cell_times_reorder),radial.pos=sort(cell_times_reorder),
            line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(cell_times_reorder)), lwd=2)

The plots of estimated gene pattern and the true gene pattern.

First co-ordinate

plot(cycle_data_reorder[order(out_np$cell_times),1], type="l")

plot(cycle_data[,1],type="l")

30th coordinate

plot(cycle_data_reorder[order(out_np$cell_times),30], type="l")

plot(cycle_data[,30],type="l")

50th coordinate

plot(cycle_data_reorder[order(out_np$cell_times),50], type="l")

plot(cycle_data[,50],type="l")